Ground-based data for PRLA

Get the time and weather conditions for all spectra from a site. Start with preferred location (buoys), then can expand (inlet, outlet, reach) where other overlapping data are available.

Updating the AOS and AIS data is handled separately in neon-aqu-aos. AOP flight times are determined from L1 radiance data.

mysite = 'PRLA'

Chlorophyll - AOS

  • From processed chl a files on Box
  • reported in ug/L
  • seasonal sampling, 2 analytes

See how many locations chl data is collected from

See how many locations chl data is collected from (variable Y axis)

Availability of AOS data for each flight date

  • Default threshold 1 = 30 days
  • Default threshold 2 = 60 days
flightdate aos_before aos_after days_before days_after min_days meets_thresh1 meets_thresh2
2016-06-29 NA 2019-07-11 NA 1107 1107 FALSE FALSE
2017-06-21 NA 2019-07-11 NA 750 750 FALSE FALSE
2017-06-26 NA 2019-07-11 NA 745 745 FALSE FALSE
2019-07-26 2019-07-11 2019-09-10 15 46 15 TRUE TRUE
2019-07-27 2019-07-11 2019-09-10 16 45 16 TRUE TRUE
2019-07-30 2019-07-11 2019-09-10 19 42 19 TRUE TRUE
2020-06-24 2020-06-15 2020-09-29 9 97 9 TRUE TRUE
2020-06-26 2020-06-15 2020-09-29 11 95 11 TRUE TRUE
2020-07-02 2020-06-15 2020-09-29 17 89 17 TRUE TRUE
flightdate aos_match days
2019-07-26 2019-07-11 15
2019-07-27 2019-07-11 16
2019-07-30 2019-07-11 19
2020-06-24 2020-06-15 9
2020-06-26 2020-06-15 11
2020-07-02 2020-06-15 17
  • Make sure plant algae lab units are all micrograms per liter
  • Check sample conditions
## [1] "microgramsPerLiter"
## [1] "condition ok"

These are the closest chl AOS values for each flight date

aos_match flightdate days pheophytin chlorophyll a
2019-07-11 2019-07-26 15 3.01 2.31
2019-07-11 2019-07-27 16 3.01 2.31
2019-07-11 2019-07-30 19 3.01 2.31
2020-06-15 2020-06-24 9 4.20 3.45
2020-06-15 2020-06-26 11 4.20 3.45
2020-06-15 2020-07-02 17 4.20 3.45

Chlorophyll - Algal Community

TO DO!!!!!

  • Relative abundance by division, class for diatom slides and soft algae count
  • Top 10 morphospecies for each method?

Chlorophyll - AIS

Sensor chl data availability

flightline_datetime check_30day check_10day check_1day check_12hr
2016-06-29 15:45:47 FALSE FALSE FALSE FALSE
2016-06-29 15:52:09 FALSE FALSE FALSE FALSE
2016-06-29 17:22:24 FALSE FALSE FALSE FALSE
2017-06-21 20:58:28 FALSE FALSE FALSE FALSE
2017-06-26 15:33:21 FALSE FALSE FALSE FALSE
2017-06-26 16:04:51 FALSE FALSE FALSE FALSE
2017-06-26 16:11:11 FALSE FALSE FALSE FALSE
2019-07-26 15:20:23 TRUE TRUE TRUE TRUE
2019-07-26 16:22:11 TRUE TRUE TRUE TRUE
2019-07-26 22:09:25 TRUE TRUE TRUE TRUE
2019-07-27 15:27:04 TRUE TRUE TRUE TRUE
2019-07-30 15:34:20 TRUE TRUE TRUE TRUE
2020-06-24 17:36:27 TRUE TRUE TRUE TRUE
2020-06-24 16:26:15 TRUE TRUE TRUE TRUE
2020-06-24 16:18:44 TRUE TRUE TRUE TRUE
2020-06-26 19:28:06 TRUE TRUE TRUE FALSE
2020-07-02 17:14:10 TRUE TRUE FALSE FALSE

Chlorophyll AIS plots 2019

  • Filtered to only 0 quality flags

Chlorophyll AIS plots 2020

  • No QF filters on these plots
  • Is QF because of lack of calibration?

Chlorophyll AIS vs AOS regression

TO DO!!!!!

DOM - AOS

  • From processed Surface water chemistry files on Box

Ignoring data before 2016

## Warning: Removed 2 rows containing missing values (geom_point).

Correct older UV Absorbance wavelengths from 250 to 254, assuming all 250 nm should be 254.

swchem_site_df <- swchem_site_df %>%
  dplyr::mutate(analyte = dplyr::case_when(analyte == 'UV Absorbance (250 nm)' ~
                                             'UV Absorbance (254 nm)', TRUE ~ analyte))
## Warning: Removed 2 rows containing missing values (geom_point).

How much does SUVA 254/280 ratio change?

How much does organic carbon dissolved proportion change?

Adjusts sample IDs in a new column to group together raw and filtered, while keeping track of duplicates

## Warning: Removed 11 rows containing missing values (geom_point).

Match DOM AOS and AOP data

flightdate aos_before aos_after days_before days_after min_days meets_thresh1 meets_thresh2
2016-06-29 2014-06-19 2016-10-19 741 112 112 FALSE FALSE
2017-06-21 2017-06-08 2017-07-06 13 15 13 TRUE TRUE
2017-06-26 2017-06-08 2017-07-06 18 10 10 TRUE TRUE
2019-07-26 2019-07-01 2019-08-06 25 11 11 TRUE TRUE
2019-07-27 2019-07-01 2019-08-06 26 10 10 TRUE TRUE
2019-07-30 2019-07-01 2019-08-06 29 7 7 TRUE TRUE
2020-06-24 2020-06-09 2020-06-30 15 6 6 TRUE TRUE
2020-06-26 2020-06-09 2020-06-30 17 4 4 TRUE TRUE
2020-07-02 2020-06-30 2020-08-04 2 33 2 TRUE TRUE
flightdate aos_match days
2017-06-21 2017-06-08 13
2017-06-26 2017-07-06 10
2019-07-26 2019-08-06 11
2019-07-27 2019-08-06 10
2019-07-30 2019-08-06 7
2020-06-24 2020-06-30 6
2020-06-26 2020-06-30 4
2020-07-02 2020-06-30 2

These are the closest CDOM-related AOS values for each flight date

  • A list of values means there are duplicate samples (multiple sampleIDs) from same date.
  • TOC is reported in milligramsPerLiter
  • Fe is reported in milligramsPerLiter
  • DOC is reported in milligramsPerLiter
  • UV abosrbance values are unitless and specific absorbance, multiply by DOC for actual absorbance
aos_match flightdate days UV Absorbance (254 nm) TOC Fe DOC UV Absorbance (280 nm)
2017-06-08 2017-06-21 13 0.5578 34.12 5e-04 29.97 0.2876
2017-07-06 2017-06-26 10 0.5566, 0.5710, 0.5653 37.87, 38.11, 38.82 5e-04, 5e-04, 5e-04 31.68, 31.81, 32.11 0.2887, 0.2961, 0.2950
2019-08-06 2019-07-26 11 0.7538 36.05 0.01 35.01 0.3852
2019-08-06 2019-07-27 10 0.7538 36.05 0.01 35.01 0.3852
2019-08-06 2019-07-30 7 0.7538 36.05 0.01 35.01 0.3852
2020-06-30 2020-06-24 6 NULL 26.05, 26.49, 26.18 NULL NULL NULL
2020-06-30 2020-06-26 4 NULL 26.05, 26.49, 26.18 NULL NULL NULL
2020-06-30 2020-07-02 2 NULL 26.05, 26.49, 26.18 NULL NULL NULL

DOM - AIS

  • availability of processed fDOM time series within different time windows
flightline_datetime check_30day check_10day check_1day check_12hr
2016-06-29 15:45:47 FALSE FALSE FALSE FALSE
2016-06-29 15:52:09 FALSE FALSE FALSE FALSE
2016-06-29 17:22:24 FALSE FALSE FALSE FALSE
2017-06-21 20:58:28 FALSE FALSE FALSE FALSE
2017-06-26 15:33:21 FALSE FALSE FALSE FALSE
2017-06-26 16:04:51 FALSE FALSE FALSE FALSE
2017-06-26 16:11:11 FALSE FALSE FALSE FALSE
2019-07-26 15:20:23 TRUE TRUE TRUE TRUE
2019-07-26 16:22:11 TRUE TRUE TRUE TRUE
2019-07-26 22:09:25 TRUE TRUE TRUE TRUE
2019-07-27 15:27:04 TRUE TRUE TRUE TRUE
2019-07-30 15:34:20 TRUE TRUE TRUE TRUE
2020-06-24 17:36:27 TRUE TRUE TRUE TRUE
2020-06-24 16:26:15 TRUE TRUE TRUE TRUE
2020-06-24 16:18:44 TRUE TRUE TRUE TRUE
2020-06-26 19:28:06 TRUE TRUE TRUE FALSE
2020-07-02 17:14:10 TRUE TRUE FALSE FALSE

fDOM plots 2019

## Warning: Removed 3170 rows containing missing values (geom_point).

## Warning: Removed 21 rows containing missing values (geom_point).

## `geom_smooth()` using method = 'loess' and formula 'y ~ x'

## `geom_smooth()` using method = 'loess' and formula 'y ~ x'

## `geom_smooth()` using method = 'loess' and formula 'y ~ x'

fDOM plots 2020

  • Not filtered on QFs
  • QF because of lack of calibration?
## Warning: Removed 8658 rows containing missing values (geom_point).

## Warning: Removed 2552 rows containing missing values (geom_point).

## Warning: Removed 444 row(s) containing missing values (geom_path).
## Warning: Removed 444 rows containing missing values (geom_point).

## Warning: Removed 4737 rows containing missing values (geom_point).

fDOM AIS vs DOC AOS regression

TO DO!!!!

Suspended Matter - AOS

  • From processed Surface water chemistry files on Box
  • TDS passes through .45 micron filter
  • TSS is from weight of dried mass that doesnt pass through filter

Data from all locations at site

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

sm_site_df <- sm_site_df %>%
  dplyr::filter(namedLocation %in% my_loc)
## Warning: Transformation introduced infinite values in continuous y-axis

## Warning: Transformation introduced infinite values in continuous y-axis

How much does TDS/TSS change?

  • Adjusts sample IDs in a new column to group together raw and filtered, while keeping track of duplicates
  • Dissolved passes through .45 micron filter, suspended does not
## Warning: Removed 1 row(s) containing missing values (geom_path).
## Warning: Removed 2 rows containing missing values (geom_point).

Match sediment aos to aop dates

source('R/match-aop-aos.R')

sm_match_list <- match_aop_aos(mysite_dates, sm_site_df, 'collect_date')

knitr::kable(sm_match_list$dates)
flightdate aos_before aos_after days_before days_after min_days meets_thresh1 meets_thresh2
2016-06-29 2014-06-19 2016-10-19 741 112 112 FALSE FALSE
2017-06-21 2017-06-08 2017-07-06 13 15 13 TRUE TRUE
2017-06-26 2017-06-08 2017-07-06 18 10 10 TRUE TRUE
2019-07-26 2019-07-01 2019-08-06 25 11 11 TRUE TRUE
2019-07-27 2019-07-01 2019-08-06 26 10 10 TRUE TRUE
2019-07-30 2019-07-01 2019-08-06 29 7 7 TRUE TRUE
2020-06-24 2019-12-04 2021-05-04 203 314 203 FALSE FALSE
2020-06-26 2019-12-04 2021-05-04 205 312 205 FALSE FALSE
2020-07-02 2019-12-04 2021-05-04 211 306 211 FALSE FALSE
knitr::kable(sm_match_list$matches)
flightdate aos_match days
2017-06-21 2017-06-08 13
2017-06-26 2017-07-06 10
2019-07-26 2019-08-06 11
2019-07-27 2019-08-06 10
2019-07-30 2019-08-06 7

List of values means there are duplicate samples (multiple sampleIDs) from same date.

aos_match flightdate days TDS TSS TSS - Dry Mass
2017-06-08 2017-06-21 13 910.1 32 800
2017-07-06 2017-06-26 10 885.62, 887.64, 891.23 10, 9, 9 900, 900, 1000
2019-08-06 2019-07-26 11 744.6 10 500
2019-08-06 2019-07-27 10 744.6 10 500
2019-08-06 2019-07-30 7 744.6 10 500

Suspended Matter - AIS

  • processed turbidity water quality time series on box
flightline_datetime check_30day check_10day check_1day check_12hr
2016-06-29 15:45:47 FALSE FALSE FALSE FALSE
2016-06-29 15:52:09 FALSE FALSE FALSE FALSE
2016-06-29 17:22:24 FALSE FALSE FALSE FALSE
2017-06-21 20:58:28 FALSE FALSE FALSE FALSE
2017-06-26 15:33:21 FALSE FALSE FALSE FALSE
2017-06-26 16:04:51 FALSE FALSE FALSE FALSE
2017-06-26 16:11:11 FALSE FALSE FALSE FALSE
2019-07-26 15:20:23 TRUE TRUE TRUE TRUE
2019-07-26 16:22:11 TRUE TRUE TRUE TRUE
2019-07-26 22:09:25 TRUE TRUE TRUE TRUE
2019-07-27 15:27:04 TRUE TRUE TRUE TRUE
2019-07-30 15:34:20 TRUE TRUE TRUE TRUE
2020-06-24 17:36:27 TRUE TRUE TRUE TRUE
2020-06-24 16:26:15 TRUE TRUE TRUE TRUE
2020-06-24 16:18:44 TRUE TRUE TRUE TRUE
2020-06-26 19:28:06 TRUE TRUE TRUE FALSE
2020-07-02 17:14:10 TRUE TRUE FALSE FALSE

Turbidity plots 2019

  • filtered to no quality flags

Turbidity plots 2020

  • Not filtered for quality flags
  • QF because of lack of calibration?
## Warning: Removed 8537 row(s) containing missing values (geom_path).
## Warning: Removed 8658 rows containing missing values (geom_point).

## Warning: Removed 2438 row(s) containing missing values (geom_path).
## Warning: Removed 2552 rows containing missing values (geom_point).

## Warning: Removed 444 row(s) containing missing values (geom_path).
## Warning: Removed 444 rows containing missing values (geom_point).

## Warning: Removed 4737 row(s) containing missing values (geom_path).
## Warning: Removed 4737 rows containing missing values (geom_point).

Turbidity AIS vs TDS and TSS AOS regression

TO DO!!!!

SUNA - AIS

  • nitrate sensor 15 minute interval time series
  • value is from a burst of readings after lamp warms up
  • error bars on these plots are std error of mean, not expanded uncertainty like for other sensors
flightline_datetime check_30day check_10day check_1day check_12hr
2016-06-29 15:45:47 FALSE FALSE FALSE FALSE
2016-06-29 15:52:09 FALSE FALSE FALSE FALSE
2016-06-29 17:22:24 FALSE FALSE FALSE FALSE
2017-06-21 20:58:28 FALSE FALSE FALSE FALSE
2017-06-26 15:33:21 FALSE FALSE FALSE FALSE
2017-06-26 16:04:51 FALSE FALSE FALSE FALSE
2017-06-26 16:11:11 FALSE FALSE FALSE FALSE
2019-07-26 15:20:23 TRUE TRUE TRUE TRUE
2019-07-26 16:22:11 TRUE TRUE TRUE TRUE
2019-07-26 22:09:25 TRUE TRUE TRUE TRUE
2019-07-27 15:27:04 TRUE TRUE TRUE TRUE
2019-07-30 15:34:20 TRUE TRUE TRUE TRUE
2020-06-24 17:36:27 TRUE TRUE TRUE TRUE
2020-06-24 16:26:15 TRUE TRUE TRUE TRUE
2020-06-24 16:18:44 TRUE TRUE TRUE TRUE
2020-06-26 19:28:06 TRUE TRUE TRUE TRUE
2020-07-02 17:14:10 TRUE TRUE TRUE TRUE
flightline_datetime check_30day check_10day check_1day check_12hr
2019-07-26 15:20:23 TRUE TRUE TRUE TRUE
2019-07-26 16:22:11 TRUE TRUE TRUE TRUE
2019-07-26 22:09:25 TRUE TRUE TRUE TRUE
2019-07-27 15:27:04 TRUE TRUE TRUE TRUE
2019-07-30 15:34:20 TRUE TRUE TRUE TRUE
2020-06-24 17:36:27 TRUE TRUE TRUE TRUE
2020-06-24 16:26:15 TRUE TRUE TRUE TRUE
2020-06-24 16:18:44 TRUE TRUE TRUE TRUE
2020-06-26 19:28:06 TRUE TRUE TRUE TRUE
2020-07-02 17:14:10 TRUE TRUE TRUE TRUE

Helper table for pulling L0 SUNA for flight dates with SUNA data. Interval is 30 days before and after

##    flightline_datetime check_30day check_10day check_1day check_12hr
## 1  2019-07-26 15:20:23        TRUE        TRUE       TRUE       TRUE
## 2  2019-07-26 16:22:11        TRUE        TRUE       TRUE       TRUE
## 3  2019-07-26 22:09:25        TRUE        TRUE       TRUE       TRUE
## 4  2019-07-27 15:27:04        TRUE        TRUE       TRUE       TRUE
## 5  2019-07-30 15:34:20        TRUE        TRUE       TRUE       TRUE
## 6  2020-06-24 17:36:27        TRUE        TRUE       TRUE       TRUE
## 7  2020-06-24 16:26:15        TRUE        TRUE       TRUE       TRUE
## 8  2020-06-24 16:18:44        TRUE        TRUE       TRUE       TRUE
## 9  2020-06-26 19:28:06        TRUE        TRUE       TRUE       TRUE
## 10 2020-07-02 17:14:10        TRUE        TRUE       TRUE       TRUE
##    interval_start interval_end
## 1      2019-06-26   2019-08-25
## 2      2019-06-26   2019-08-25
## 3      2019-06-26   2019-08-25
## 4      2019-06-27   2019-08-26
## 5      2019-06-30   2019-08-29
## 6      2020-05-25   2020-07-24
## 7      2020-05-25   2020-07-24
## 8      2020-05-25   2020-07-24
## 9      2020-05-27   2020-07-26
## 10     2020-06-02   2020-08-01

SUNA plots 2019

  • filtered to no Quality Flags

SUNA plots 2020

  • Not filtered by QFs
  • QF because of lack of calibration?

SUNA level 0 absorbances

SUNA vs AOS absorbs

TO DO!!!

  • how do absorbances from nitrate sensor compare to AOS samples?